Hi all,
I used Cufflinks in the following work-flow:
CuffLinks -> CuffCompare -> CuffDiff
The output file genes.fpkm_tracking didn't include reference genes at all:
Even though the combined.gtf that was created in CuffCompare did contain a lot overlaps with the known genes. Also the isoforms.fpkm_tracking output file DID contain reference annotations, but in the level of exons:
* Of course, when I only ran CuffDiff with the reference GTF - I got gene expression levels with the known genes.
My questions is:
Is there a way to get gene (and not exon) expression levels AND novel transcripts using Cufflinks?
And why in the genes.fpkm_tracking file I don't get the closest reference annotation to that gene?
Thanks!
Rachelly.
I used Cufflinks in the following work-flow:
CuffLinks -> CuffCompare -> CuffDiff
The output file genes.fpkm_tracking didn't include reference genes at all:
Code:
tracking_id class_code nearest_ref_id gene_short_name tss_id locus MM_FPKM MM_conf_lo MM_conf_hi LOG_FPKM LOG_conf_lo LOG_conf_hi SFT_FPKM SFT_conf_lo SFT_conf_hi NY_FPKMNY_conf_lo NY_conf_hi XLOC_000001 - - - - SL2.30ch00:551338-551631 1.66555 0 4.24667 0.446456 0 1.7828 0.841447 0 2.67606 0 0 0 XLOC_000002 - - - - SL2.30ch00:4196781-4198207 122.746 100.586 144.907 185.302 158.075 212.529 121.462 99.1515 143.773 1616.46 1469.49 1763.43
Code:
tracking_id class_code nearest_ref_id gene_short_name tss_id locus MM_FPKM MM_conf_lo MM_conf_hi LOG_FPKM LOG_conf_lo LOG_conf_hi SFT_FPKM SFT_conf_lo SFT_conf_hi NY_FPKMNY_conf_lo NY_conf_hi TCONS_00000001 = exon:Solyc00g005040.1.1.3 - - SL2.30ch00:551338-551631 1.66555 0 4.24667 0.446456 0 1.7828 0.841447 0 2.67606 0 0 0 TCONS_00000002 o exon:Solyc00g006470.1.1.4 - - SL2.30ch00:4196781-4198207 62.9947 47.1187 78.8707 95.0768 75.573 114.581 52.5381 37.9501 67.126 972.538 908.856 1036.22
My questions is:
Is there a way to get gene (and not exon) expression levels AND novel transcripts using Cufflinks?
And why in the genes.fpkm_tracking file I don't get the closest reference annotation to that gene?
Thanks!
Rachelly.
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